Tracing Early Evolutionary History

Box 5.1 Evolutionary Trees

The University of California Museum of Paleontology provides a good general resource that includes an introduction to phylogenetic trees, homology, and related concepts. There are also teaching resources there.

The “Tree Thinking Group” at the University of Pittsburgh also has some good resources, including some excellent teaching materials.

The Concept of Descent with Modification Can Be Used to Infer Evolutionary Relationships

The inference of phylogenetic history is discussed in detail in Chapter 27. In this chapter we introduce some of the key aspects of this inference. We focus here on the general concept of working backward from comparisons of modern organisms and on how this can be done if one assumes that the path of evolution is by vertical descent. The occurrence of lateral gene transfer (see later in the chapter) complicates the reconstruction of evolutionary history somewhat.

For more on homology and analogy, try the University of California Museum of Paleontology’s web resource.

A useful discussion on convergence and parallel evolution can be found here.

Universal Homologies, LUCA, and the Tree of Life

The Existence of Universal Homologies Implies a Single Origin of Life and the Existence of LUCA

Two good papers on this topic are Kyrpides et al. (1999), which discusses using universal protein families to infer properties of LUCA, and Harris et al. (2003), which uses comparative genomics to infer the genetic core of the universal ancestor.

The Features of LUCA Can Be Inferred from Universal Character States or by Evolutionary Reconstructions

Character State Reconstruction

A good description of the phylogenetic methods for inferring the evolutionary history and processes of change in discretely valued characters can be found in Maddison (1994). In addition, a very helpful resource is the book that accompanies the computer software MacClade (e.g., Maddison and Maddison [2000]). Another useful paper is Cunningham et al. (1998), which contains a critical reappraisal of ancestral character states reconstruction.

Nonuniversal Genetic Code

A review of the “escaped triplet theory” as a possible origin of the genetic code is presented in Yarus et al (2005). Recent evidence for evolution of the genetic code is presented by Osawa et al. (1992).

Box 5.2 The Tree of Life: A Brief History

There are numerous resources available that delve more deeply into the history of tree of life studies. A good overview can be found in the Introduction to Assembling the Tree of Life (Cracraft and Donoghue 2004).

Some of the original sources mentioned in Box 5.2 are Generelle Morphologie der Organismen by Haeckel (1866), Titres et Travaux Scientifiques by Chatton (1937), and a paper by Whittaker (1969), entitled “New concepts of kingdoms of organisms.”

The important contributions of Carl Woese and his colleagues, who in analyzing the sequences of rRNA uncovered the existence of the Archaea, are detailed in many papers. Woese (1987) is still relevant and has a great discussion of rRNA, the history of phylogeny, and more. One of the first papers to show that rRNA cataloguing is useful for phylogeny was Fox et al. (1977). In Woese and Fox (1977) evidence for the existence of the Archaea is presented. The full text is available online. More evidence for the Archaea is in Woese et al. (1977). A formal proposal for constructing a system of organisms based on three domains: the Bacteria, the Archaea, and the Eukarya, is in Woese et al. (1990).

To Infer Properties of LUCA, We Need a Rooted Tree of Life

Inferring Nuclear Membrane Origins

Initial Attempts to Root the Tree of Life Suggested That Archaea and Eukaryotes Are Sister Groups

Orthologs and Paralogs

The original definition of orthologs and paralogs is from Fitch (1970). A good overview of orthologs and paralogs can be found in Koonin (2005).

Rooting the Tree with Duplicated Genes

Iwabe et al. (1989) presents the use of duplicated genes EF-TU and EFG and ATPase α and β to infer the root of the tree of life. Gogarten et al. (1989) look at the evolution of ATPases to do the same thing.

Brown and Doolittle (1997) present a detailed analysis of the phylogeny of many gene families and what they mean for the rooting of the tree and the origin of eukaryotes.

Rivera and Lake (2004) discuss the “ring of life” and some of the challenges in studying the relationships among the three domains.

The Occurrence of Gene Transfer between Species Means That Different Genes May Have Their Own LUCAs

An excellent overview of lateral gene transfer and what it could mean in phylogenetic classification can be found in Doolittle (1999). Eisen (2000) discusses genomic evidence for and against lateral gene transfer.

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